/* snpUi.c - char arrays for snp UI features */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "snpUi.h" #include "common.h" /****** Some stuff for snp colors *******/ char *snpColorLabel[] = { "red", "green", "blue", "black", "exclude", }; int snpColorLabelSize = ArraySize(snpColorLabel); /****** Some stuff for snpMapSource related controls *******/ /* dbSnp, Affy10K, Affy10Kv2, Affy50K_HindIII, Affy50K_XbaI */ char *snpMapSourceLabels[] = { "Bac Overlaps", "Random", "Mixed", "Other", "Affymetrix Genotyping Array 10K", "Affymetrix Genotyping Array 120K", }; char *snpMapSourceStrings[] = { "snpMapSourceBacOverlap", "snpMapSourceRandom", "snpMapSourceMixed", "snpMapSourceOther", "snpMapSourceAffy10K", "snpMapSourceAffy120K", }; char *snpMapSourceDataName[] = { "BAC_OVERLAP", "RANDOM", "MIXED", "OTHER", "Affy10K", "Affy120K", }; char *snpMapSourceDefault[] = { "black", "blue", "red", "red", "green", "green", }; char *snpMapSourceCart[] = { "black", "blue", "red", "red", "green", "green", }; int snpMapSourceLabelsSize = ArraySize(snpMapSourceLabels); int snpMapSourceStringsSize = ArraySize(snpMapSourceStrings); int snpMapSourceDataNameSize = ArraySize(snpMapSourceDataName); int snpMapSourceDefaultSize = ArraySize(snpMapSourceDefault); int snpMapSourceCartSize = ArraySize(snpMapSourceCart); /****** Some stuff for snpMapType related controls *******/ /* SingleNP, indel, segnemtal */ char *snpMapTypeLabel[] = { "include", "exclude", }; char *snpMapTypeLabels[] = { "Single Nucleotide Polymorphisms", "Insertions and Deletions", "Segmental Duplications", }; char *snpMapTypeStrings[] = { "snpMapTypeSingle", "snpMapTypeIndels", "snpMapTypeSegmental", }; char *snpMapTypeDataName[] = { "SNP", "INDEL", "SEGMENTAL", }; char *snpMapTypeDefault[] = { "include", "include", "include", }; char *snpMapTypeCart[] = { "include", "include", "include", }; int snpMapTypeLabelSize = ArraySize(snpMapTypeLabel); int snpMapTypeLabelsSize = ArraySize(snpMapTypeLabels); int snpMapTypeStringsSize = ArraySize(snpMapTypeStrings); int snpMapTypeDataNameSize = ArraySize(snpMapTypeDataName); int snpMapTypeDefaultSize = ArraySize(snpMapTypeDefault); int snpMapTypeCartSize = ArraySize(snpMapTypeCart); /****** Some stuff for snpColorSource related controls *******/ /* Source, Molecule Type, Class, Validation, Function */ char *snpColorSourceLabels[] = { "Source", "Molecule Type", "Variant Class", "Validation Status", "Functional Class", "Location Type", "Black", }; char *snpColorSourceStrings[] = { "snpColorSourceSource", "snpColorSourceMolType", "snpColorSourceClass", "snpColorSourceValid", "snpColorSourceFunc", "snpColorSourceLocType", "snpColorSourceBlack", }; char *snpColorSourceDataName[] = { "snpColorSource", }; char *snpColorSourceDefault[] = { "snpColorSourceFunc", }; char *snpColorSourceCart[] = { "snpColorSourceFunc", }; int snpColorSourceLabelsSize = ArraySize(snpColorSourceLabels); int snpColorSourceStringsSize = ArraySize(snpColorSourceStrings); int snpColorSourceDataNameSize = ArraySize(snpColorSourceDataName); int snpColorSourceDefaultSize = ArraySize(snpColorSourceDefault); int snpColorSourceCartSize = ArraySize(snpColorSourceCart); /****** Some stuff for snpSource related controls *******/ /* dbSnp, Affy10K, Affy10Kv2, Affy50K_HindIII, Affy50K_XbaI */ char *snpSourceLabels[] = { "dbSnp", "Affymetrix Genotyping Array 10K", "Affymetrix Genotyping Array 10K v2", "Affymetrix Genotyping Array 50K HindIII", "Affymetrix Genotyping Array 50K XbaI", }; char *snpSourceStrings[] = { "snpSourceDbSnp", "snpSourceAffy10K", "snpSourceAffy10Kv2", "snpSourceAffy50KHindIII", "snpSourceAffy50KXbaI", }; char *snpSourceDataName[] = { "dbSnp", "Affy10K", "Affy10Kv2", "Affy50K_HindIII", "Affy50K_XbaI", }; char *snpSourceDefault[] = { "black", "blue", "red", "green", "green", }; char *snpSourceCart[] = { "black", "blue", "red", "green", "green", }; int snpSourceLabelsSize = ArraySize(snpSourceLabels); int snpSourceStringsSize = ArraySize(snpSourceStrings); int snpSourceDataNameSize = ArraySize(snpSourceDataName); int snpSourceDefaultSize = ArraySize(snpSourceDefault); int snpSourceCartSize = ArraySize(snpSourceCart); /****** Some stuff for snpMolType related controls *******/ /* unknown, genomic, cDNA, mito, chloro */ char *snpMolTypeLabels[] = { "Unknown", "Genomic", "cDNA", "Mitochondrial", "Chloroplast", }; char *snpMolTypeStrings[] = { "snpMolTypeUnknown", "snpMolTypeGenomic", "snpMolTypecDNA", "snpMolTypeMito", "snpMolTypeChloro", }; char *snpMolTypeDataName[] = { "unknown", "genomic", "cDNA", "mito", "chloro", }; char *snpMolTypeDefault[] = { "red", "black", "blue", "green", "exclude", }; char *snpMolTypeCart[] = { "red", "black", "blue", "green", "exclude", }; int snpMolTypeLabelsSize = ArraySize(snpMolTypeLabels); int snpMolTypeStringsSize = ArraySize(snpMolTypeStrings); int snpMolTypeDataNameSize = ArraySize(snpMolTypeDataName); int snpMolTypeDefaultSize = ArraySize(snpMolTypeDefault); int snpMolTypeCartSize = ArraySize(snpMolTypeCart); /****** Some stuff for snpClass related controls *******/ /* unknown, snp, in-del, het, microsat, named, no-variation, mixed, * mnp */ char *snpClassLabels[] = { "Unknown", "Single Nucleotide Polymorphism", "Insertion / Deletion", "Heterozygous", "Microsatellite", "Named", "No Variation", "Mixed", "Multiple Nucleotide Polymorphism", }; char *snpClassStrings[] = { "snpClassUnknown", "snpClassSnp", "snpClassInDel", "snpClassHet", "snpClassMicrosat", "snpClassNamed", "snpClassNoVariation", "snpClassMixed", "snpClassMnp", }; char *snpClassDataName[] = { "unknown", "snp", "in-del", "het", "microsat", "named", "no-variation", "mixed", "mnp", }; char *snpClassDefault[] = { "red", "black", "blue", "red", "green", "green", "red", "black", "blue", }; char *snpClassCart[] = { "red", "black", "blue", "red", "green", "green", "red", "black", "blue", }; int snpClassLabelsSize = ArraySize(snpClassLabels); int snpClassStringsSize = ArraySize(snpClassStrings); int snpClassDataNameSize = ArraySize(snpClassDataName); int snpClassDefaultSize = ArraySize(snpClassDefault); int snpClassCartSize = ArraySize(snpClassCart); /****** Some stuff for snpValid related controls *******/ /* unknown, other-pop, by-frequency, by-cluster, by-2hit-2allele, * by-hapmap, genotype */ char *snpValidLabels[] = { "Unknown", "Other Population", "By Frequency", "By Cluster", "By 2 Hit / 2 Allele", "By HapMap", "By Genotype", }; char *snpValidStrings[] = { "snpValidUnknown", "snpValidOtherPop", "snpValidFrequency", "snpValidCluster", "snpValid2H2A", "snpValidHapMap", "snpValidGenotype", }; char *snpValidDataName[] = { "unknown", "other-pop", "by-frequency", "by-cluster", "by-2hit-2allele", "by-hapmap", "genotype", }; char *snpValidDefault[] = { "red", "black", "black", "black", "black", "blue", "green", }; char *snpValidCart[] = { "red", "black", "black", "black", "black", "blue", "green", }; int snpValidLabelsSize = ArraySize(snpValidLabels); int snpValidStringsSize = ArraySize(snpValidStrings); int snpValidDataNameSize = ArraySize(snpValidDataName); int snpValidDefaultSize = ArraySize(snpValidDefault); int snpValidCartSize = ArraySize(snpValidCart); /****** Some stuff for snpFunc related controls *******/ /* unknown, locus-region, coding, coding-synon, coding-nonsynon, * mrna-utr, intron, splice-site, reference, exception */ char *snpFuncLabels[] = { "Unknown", "Locus Region", "Coding", "Coding - Synonymous", "Coding - Non-Synonymous", "mRNA/UTR", "Intron", "Splice site", "Reference", "Exception", }; char *snpFuncStrings[] = { "snpFuncUnknown", "snpFuncLocus", "snpFuncCoding", "snpFuncSynon", "snpFuncNonSynon", "snpFuncmRnaUtr", "snpFuncIntron", "snpFuncSplice", "snpFuncReference", "snpFuncException", }; char *snpFuncDataName[] = { "unknown", "locus-region", "coding", "coding-synon", "coding-nonsynon", "mrna-utr", "intron", "splice-site", "reference", "exception", }; char *snpFuncDefault[] = { "black", "black", "blue", "green", "red", "blue", "blue", "red", "black", "black", }; char *snpFuncCart[] = { "black", "black", "blue", "green", "red", "blue", "blue", "red", "black", "black", }; int snpFuncLabelsSize = ArraySize(snpFuncLabels); int snpFuncStringsSize = ArraySize(snpFuncStrings); int snpFuncDataNameSize = ArraySize(snpFuncDataName); int snpFuncDefaultSize = ArraySize(snpFuncDefault); int snpFuncCartSize = ArraySize(snpFuncCart); /****** Some stuff for snpLocType related controls *******/ /* unknown, range, exact, between */ char *snpLocTypeLabels[] = { "Unknown", "Range", "Exact", "Between", }; char *snpLocTypeStrings[] = { "snpLocTypeUnknown", "snpLocTypeRange", "snpLocTypeExact", "snpLocTypeBetween", }; char *snpLocTypeDataName[] = { "unknown", "range", "exact", "between", }; char *snpLocTypeDefault[] = { "red", "green", "blue", "black", }; char *snpLocTypeCart[] = { "red", "green", "blue", "black", }; int snpLocTypeLabelsSize = ArraySize(snpLocTypeLabels); int snpLocTypeStringsSize = ArraySize(snpLocTypeStrings); int snpLocTypeDataNameSize = ArraySize(snpLocTypeDataName); int snpLocTypeDefaultSize = ArraySize(snpLocTypeDefault); int snpLocTypeCartSize = ArraySize(snpLocTypeCart); /****** Some stuff for snpLocType related controls *******/ /* minimum Average Heterozygosity cutoff */ float snpAvHetCutoff = 0.0;